qqnorm.gls {nlme} | R Documentation

## Normal Plot of Residuals from a gls Object

### Description

Diagnostic plots for assessing the normality of residuals the generalized least squares fit are obtained. The `form` argument gives considerable flexibility in the type of plot specification. A conditioning expression (on the right side of a `|` operator) always implies that different panels are used for each level of the conditioning factor, according to a Trellis display.

### Usage

    ## S3 method for class 'gls':
    qqnorm(y, form, abline, id, idLabels, grid, ...)

### Arguments

`y` | an object inheriting from class `gls`, representing a generalized least squares fitted model.

`form`

an optional one-sided formula specifying the desired type of plot. Any variable present in the original data frame used to obtain `y` can be referenced. In addition, `y` itself can be referenced in the formula using the symbol `"."`. Conditional expressions on the right of a `|` operator can be used to define separate panels in a Trellis display. The expression on the right hand side of `form` and to the left of a `|` operator must evaluate to a residuals vector. Default is `~ resid(., type = "p")`, corresponding to a normal plot of the standardized residuals.

`abline` | an optional numeric value, or numeric vector of length two. If given as a single value, a horizontal line will be added to the plot at that coordinate; else, if given as a vector, its values are used as the intercept and slope for a line added to the plot. If missing, no lines are added to the plot.

`id`

an optional numeric value, or one-sided formula. If given as a value, it is used as a significance level for a two-sided outlier test for the standardized residuals (random effects). Observations with absolute standardized residuals (random effects) greater than the 1 - value/2 quantile of the standard normal distribution are identified in the plot using `idLabels`. If given as a one-sided formula, its right hand side must evaluate to a logical, integer, or character vector which is used to identify observations in the plot. If missing, no observations are identified.

`idLabels` | an optional vector, or one-sided formula. If given as a vector, it is converted to character and used to label the observations identified according to `id`. If given as a one-sided formula, its right hand side must evaluate to a vector which is converted to character and used to label the identified observations. Default is the innermost grouping factor.
`grid` | an optional logical value indicating whether a grid should be added to plot. Default depends on the type of Trellis plot used: if `xyplot` defaults to `TRUE`, else defaults to `FALSE`.
`...` | optional arguments passed to the Trellis plot function.

### Value

a diagnostic Trellis plot for assessing normality of residuals.

### Author(s)

Jose Pinheiro Jose.Pinheiro@pharma.novartis.com and Douglas Bates bates@stat.wisc.edu

### See Also

`gls`, `plot.gls`

### Examples

    data(Ovary)
    fm1 <- gls(follicles ~ sin(2*pi*Time) + cos(2*pi*Time), Ovary,
               correlation = corAR1(form = ~ 1 | Mare))
    qqnorm(fm1, abline = c(0,1))

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